First, once you've made it to Newark Penn, I think it takes much longer to take the PATH to mid-town Manhattan than to take the regular NJTransit trains from Newark Penn to NY Penn station in mid-town. And there's much higher frequency of trains from Newark Penn into NY Penn than from Maplewood into NY Penn - (so there is a "train reason" to ride to Newark, even if don't plan to take the PATH).

Downtown Newark, especially around Penn station, does not strike me as very "bike friendly" -- unless you ride on the sidewalks -- not how I prefer to ride my bike, but Newark around Penn station is one of the few places that inspires me more toward that mode.

"bad areas" -- Might depend on what route you take.
If you're thinking of crime, there probably will be people who will tell you that X location is dangerous -- but that doesn't mean they have much recent relevant data (which distinguishes crime against people in vehicles passing through versus crime by local residents against each other).

I've skated or biked around in Newark on random days in full daylight and good weather and never had any problem. What it's like in the dark on which streets, I don't know much about that.

Ken